Here it is:
As far as the Judge system goes, it may be too complicated to adapt in that form to an MMO. In FFTA (I only played a dozen or so hours of FFT. Tough to go back to that one if you played and got used to hundreds of hours of the mobile versions!) I would often sit for a few minutes and carefully choose exactly which team member I wanted for even trivial battles because you'd have to consider the rules that have been placed on combat, what weapons you currently had equipped, what class all of your characters were and making sure you had a good balance as well as making sure you had the characters in there with abilities you were trying to train up. In a single player turn based strategy game, you have all the time in the world to decide what you'll do each turn as well as to prepare for each fight. Obviously, the situation changes when you turn that game play into an MMO. In certain ways, you have to "dumb down" the strategy, at least on the surface. In order to show the players what they need to know, you need a sort of visual shorthand. Whereas in FFT they would tell the player directly "No Ranged Attacks" or "No Magic Attacks", in Pirate, they tell you indirectly by just not having any ranged characters show up or any magic characters show up. The result is similar, but requires less planning as other players wait for you to pick through 30 crew members :-)
In MMO's, it has been my experience that most of the strategy takes place before you even leave your house, so to speak: you set your equipment up with the right enchantments/gems, make sure all the right stats are boosted, arrange your ability bar, go to trainers, get a pack full of potions, etc . . . Then , when you go out to fight, it's just a button mash if it's solo grinding or maybe a complicated dance routine if you're with a raid fighting a big boss battle. In Pirate 101, and the same could be said of Wizard 101, you at least have 30 to make decisions based on what has just occurred in the fight. It doesn't seem like a lot, but unless you got up to make sandwiches while all the battle animations took place, you're thinking what your next moves will be.
Granted: I am only lvl 14 in the game, didn't play in Alpha or Beta, so I haven't experienced anything at a higher level, so it may get more complicated further down the road. My opinion is solely based on what I've experienced up to Monquista. That being said, I haven't had any issues with the time limit. You only have, at most, 4 chess pieces to manage and, at least at this level, most of the abilities my crew has are reactionary, so it's more about hoping they get attacked in the right way :-) Your pirate is the most complicated, but also what you have spent the most time updating and what you are the most used to since they are in every single battle.
So, I haven't run into any issues with the time limit yet, but I do understand why they did it. I hate waiting for everyone else to decide what to do for another 15 seconds (especially if there is only 1 mob left. What's to decide?) and I can't imagine what it would be like if they increased that. Companion management is a huge part of the game strategy and I would like to see a bit more depth there (I like equipping everyone's gear. The more the merrier!), but other that a bit more out-of-combat depth, I don't see too many ways they could add more depth, but here are a few that don't require much explaination: terrain and direction. I think it's fun to flank an enemy, though I hate when it's done to me, but having what direction a character is facing when attacked matter is a good way to go. Also, multi-level playing fields or characters being having to move slower through snow, or fighting better on pavement could add a lot more depth to combat. The more stuff like this you add, the more time you need to really think things out. There's no easy answer and I think they've done a fine job coming up with a solution. The nice thing about MMO's is that if they think of something better, they can always add it later!